I'm trying to publish a webapp to a server. The way we do this at my work is we publish it to a local folder on whatever computer we're working on and then upload the contents of that folder (except the web.config file) to the root folder on the server. This seems to work fine, so I'm trying to do the same on my home computer and my own server.

I`m working in Visual Studios Express 2012 for Web. My Server is Windows Server 2003 running IIS 6. It publishes in C:\inetpub\wwwroot\DefaultAppPool\ and if I go to http://localhost/DefaultAppPool/ it seems to work fine. Then I upload to D:\Inetpub\public_websites\mm-theory\wwwroot\. There are two web.config files, one outside the DefaultAppPool folder that looks like this:

Server Error in '/' Application.
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Parser Error
Description: An error occurred during the parsing of a resource required to service this request. Please review the following specific parse error details and modify your source file appropriately.